Abstract

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. We have performed a systematic and extensive evaluation of a number of different protein force fields based on comparisons of experimental data with molecular dynamics simulations. We then selected one of the most recent and accurate force fields to perform molecular dynamics simulations (over periods ranging between 100 µs and 1 ms) of the folding of 12 structurally diverse proteins. In the simulations, the proteins, representing all three major structural classes, spontaneously and repeatedly folded to their experimentally determined native structures. I will present the results of the analyses we performed to identify the common principles that underlie the folding of these proteins. We found that early in the folding process, the protein backbone adopts a native-like topology while certain secondary structure elements and a small number of non-local contacts form. In most cases, folding follows a single dominant route, in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.